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Tutorial script with working paths and command lines

November 5, 2012 in Problem Sets

The slides on the website present the proper command line arguments for the java tools.

These examples also remind you to run qsub -I before starting your work.
I also have added modules to the biocluster system now so you don’t have the set the GATK and PICARD environment variables.
you would simply do
module load picard
module load GATK
and now you can run the gatk with
java -Xmx2g -jar $GATK …
or picard tools with
java -Xmx2g -jar $PICARD/SortSam.jar I=In.sam O=Out.bam SORT_ORDER=coordinate
I have written a file which pretty much does the whole tutorial for you in a single shell script. You can experiment with this. One option is for you to work on downloading a different dataset and then comparing two strains to each other.  When you run GATK UnifiedGenotyper you will want to provide multiple BAM files which are the different strains.

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